Much of Vaati's Palace is covered in holes and ledges. Also, the enemies found here are stronger and more numerous than in previous stages.

On the Silver Door, all three stages take place in the actual Palace itself. On the Gold Door, the first two stages take place in the Sea of Trees, Talus Cave, or Death Mountain, before the third being in the Palace. The Hero Door consists of twelve stages as opposed to three stages, adding difficulty to the level itself.

Regardless of key and after travelling through Vaati's Palace, the Links meet up with and ultimately duel Vaati. After Vaati's defeat, the Links are reunited with Zelda.